Comparison between pollen counts at ground and at roof level in Basel (Switzerland)

Measurements of pollen frequency were made using two identical pollen traps, one situated at ground level and one at the height of about 30 m. There was no special difference between the results for the two traps in 1995, apart from an excess of pollen in the ground level trap originatinig from trees growing near the trap. In 1996 there was also a greater amount of birch pollen, this time at the roof level. There was also a great difference in the time at which the pollen first appeared between the two years, especially in the early spring.     

A new sub-sampling method for analysis of air samples collected with the Andersen single-stage sampler

A protocol for bioaerosol collection was developed that provides not only accurate predictions of fungal concentration, but also improves species recovery. Random transfer of a subset of 50 of the 400 impaction points from Andersen single-stage bioaerosol sampling plates results in subcultures that are accurate predictors of fungal concentration (CFU/m³), when compared to duplicate untouched Andersen plates. A linear regression model was developed to estimate CFU/m³ from the colonies counted on the Random-50 plates. The random transfer to five plates (“Random-50” plates), allows large numbers of fungi to be recovered and identified, including slow-growing fungi that otherwise would be masked by fast-growing fungi.     

Analyzing the D-amino acid content in biological samples by engineered enzymes

The aim of our present research is to produce mutant forms of D-amino acid oxidase from Rhodotorula gracilis in order to determine D-amino acid content in different biological samples. During the past few years, our group has produced yeast D-amino acid oxidase variants with altered substrate specificity (e.g., active on acidic, or hydrophobic, or on all D-amino acids) both by rational design and directed evolution methods. Now, the kinetic constants for a number of amino acids (even for unnatural ones) of the most relevant D-amino acid oxidase variants have been investigated. This information constitutes the basis for considering potential analytical applications in this important field.     

Escherichia coli in settled-dust and air samples collected in residential environments in Mexico City.

Escherichia coli, an important indicator of the presence of fecal material, was isolated from indoor and outdoor environments in Mexico City. The heterogeneity of E. coli was represented by 89 serotypes, most of them coming from settled-dust indoor samples; 21% of them presented antibiotic multiresistance. The numbers of plasmids were higher among the antibiotic-resistant strains. The results of this study suggest that intestinal infections produced by environmental strains could be of more epidemiological impact than previously thought.     

3'-Half of the thrombopoietin cDNA confers higher expression of erythropoietin at the RNA level but not at the protein level

Both erythropoietin (EPO) and the short-form thrombopoietin (TPO) were expressed at low levels whereas the long-form TPO was expressed at high levels in transgenic animals. To elucidate the role of carboxy-terminal half of the long-form TPO which is absent in the short-form, we generated recombinant TPO or EPO expression vectors which contain or lack the carboxy-terminal half of TPO and examined their expression in the HC11 and 293 cells. The long-form TPO was expressed higher than the short-form regardless of the cell types, transfection modes, and promoters. When 3'-half of the long-form TPO cDNA was placed downstream of the EPO cDNA to act as a 3'-untranslated region, expression of EPO was moderately increased at the RNA level, however, no remarkable increase was observed at the protein level. These results suggest that the low expression of EPO, as like as the short-form TPO, is due to absence of the 3'-half in the full-length TPO that confers stability both at the RNA and protein levels.     

Robust and simplified machine learning identification of pitfall trap‐collected ground beetles at the continental scale

1. Insect populations are changing rapidly, and monitoring these changes is essential for understanding the causes and consequences of such shifts. However, large‐scale insect identification projects are time‐consuming and expensive when done solely by human identifiers. Machine learning offers a possible solution to help collect insect data quickly and efficiently.
2. Here, we outline a methodology for training classification models to identify pitfall trap‐collected insects from image data and then apply the method to identify ground beetles (Carabidae). All beetles were collected by the National Ecological Observatory Network (NEON), a continental scale ecological monitoring project with sites across the United States. We describe the procedures for image collection, image data extraction, data preparation, and model training, and compare the performance of five machine learning algorithms and two classification methods (hierarchical vs. single‐level) identifying ground beetles from the species to subfamily level. All models were trained using pre‐extracted feature vectors, not raw image data. Our methodology allows for data to be extracted from multiple individuals within the same image thus enhancing time efficiency, utilizes relatively simple models that allow for direct assessment of model performance, and can be performed on relatively small datasets.
3. The best performing algorithm, linear discriminant analysis (LDA), reached an accuracy of 84.6% at the species level when naively identifying species, which was further increased to >95% when classifications were limited by known local species pools. Model performance was negatively correlated with taxonomic specificity, with the LDA model reaching an accuracy of ~99% at the subfamily level. When classifying carabid species not included in the training dataset at higher taxonomic levels species, the models performed significantly better than if classifications were made randomly. We also observed greater performance when classifications were made using the hierarchical classification method compared to the single‐level classification method at higher taxonomic levels.
4. The general methodology outlined here serves as a proof‐of‐concept for classifying pitfall trap‐collected organisms using machine learning algorithms, and the image data extraction methodology may be used for nonmachine learning uses. We propose that integration of machine learning in large‐scale identification pipelines will increase efficiency and lead to a greater flow of insect macroecological data, with the potential to be expanded for use with other noninsect taxa.

     

Development of a monitoring network for the analysis of elements in aerosol samples collected at Lake Balaton

Determination of different toxic elements in aerosol and precipitation samples collected at Lake Balaton were carried out. A simple sequential leaching procedure was applied for the determination of the distribution of elements. The distribution of elements was determined among environmentally mobile, bound to carbonates and oxides, and bound to silicates and organic matters (environmentally immobile) fractions. Particular attention was paid to distinguish between environmentally mobile and environmentally immobile fractions because these represent the two extreme modes by which the metals are bound to the solid matrices. Aerosol samples were weekly collected in Tihany, Siófok and Keszthely on 5 cm diameter Teflon filters with a membrane pump. While Cd-compounds have been found enormously in the environmentally mobile fractions, As-compounds accumulated almost evenly among portions. The results of sequential leaching give an indication of the mobility of the elements once the aerosol is mixed directly into natural waters on during scavenging of the aerosol by wet deposition. Based upon the data it can be concluded that the effect of anthropogenic sources is minor in this area.     

Fungal content of air samples from some asthmatic childrens’ homes in Mexico City

Fungal particles can be considered a potential risk factor in children causing asthma, rhinitis, and allergy. However, a direct relationship between mold exposure and respiratory symptoms is difficult to establish, particularly if volumetric results are not well documented, as is often the case in Mexico. In order to assess mold exposure in some asthmatic childrens’ homes, eight asthmatic children were selected. For each child, lung function was measured by spirometry and the flow expiratory volume drop in the first second (FEV₁) as well as the CVF were estimated at 5, 10 and 15 min, after a running period on a treadmill. Exercise induced asthma (EIA) was defined as a FEV₁ drop <10% or FEV₁/CVF drop >10%. Atopy was estimated by skin testing of allergen extracts. Each room was volumetrically sampled using Burkard Personal samplers, every week for a month and with different degrees of activity. Fungal composition was mostly dominated by allergenic molds, spores smaller than 10 μm and non-seasonal molds. Concentrations ranged from 0 to 2087 CFU/m³ and 102 553–29 522 200 spores/m³, being significantly higher in indoor air, but the differences between rooms or weeks were not significant, either for CFUs (P>0.27) or for total particles (P>0.80). In general, mold counts were dominated byPenicillium spp. andCladosporium spp. especiallyP. aurantiogriseum andC. cladosporioides. We observed that the median concentration values were in general higher for children with exercise induced asthma (EIA). But the differences were significant only for EIA and degree, of asthma particularly for total (P=0.038), mycotoxin producers (P<0.009), seasonal molds (P<0.006) andPenicillium spp. (P=0.012). Total spore counts showed the highest median values in children without EIA, moderate asthma degree and no atopy. Significant differences were found for almost all spore, type groupings when comparing the presence of EIA (P<0.05) or asthma degree categories (P<0.030), but no differences were observed for atopy (P>0.21). We conclude that respiratory symptoms as described by EIA, asthma severity and atopy may give a good correlation with fungal concentrations and especially comparisons based on their physical and chemical properties.     

The handedness or chirality of biological structure at the molecular and at higher levels of structural organisation.

The relationship between chiral bias at the molecular and at higher levels of structural organisation is discussed. The discussion is based on observations made on collagen and in particular on elastoidin fibres.     

Quantification of NADH:ubiquinone oxidoreductase (complex I) content in biological samples

Impairments in mitochondrial energy metabolism have been implicated in human genetic diseases associated with mitochondrial and nuclear DNA mutations, neurodegenerative and cardiovascular disorders, diabetes, and aging. Alteration in mitochondrial complex I structure and activity has been shown to play a key role in Parkinson''s disease and ischemia/reperfusion tissue injury, but significant difficulty remains in assessing the content of this enzyme complex in a given sample. The present study introduces a new method utilizing native polyacrylamide gel electrophoresis in combination with flavin fluorescence scanning to measure the absolute content of complex I, as well as α-ketoglutarate dehydrogenase complex, in any preparation. We show that complex I content is 19 ± 1 pmol/mg of protein in the brain mitochondria, whereas varies up to 10-fold in different mouse tissues. Together with the measurements of NADH-dependent specific activity, our method also allows accurate determination of complex I catalytic turnover, which was calculated as 10⁴ min⁻¹ for NADH:ubiquinone reductase in mouse brain mitochondrial preparations. α-ketoglutarate dehydrogenase complex content was determined to be 65 ± 5 and 123 ± 9 pmol/mg protein for mouse brain and bovine heart mitochondria, respectively. Our approach can also be extended to cultured cells, and we demonstrated that about 90 × 10³ complex I molecules are present in a single human embryonic kidney 293 cell. The ability to determine complex I content should provide a valuable tool to investigate the enzyme status in samples after in vivo treatment in mutant organisms, cells in culture, or human biopsies.     

A simple device for harvesting biological fluids at the microscopic level

A simple aspirating device is described which permits repeated samples of biological materials to be taken near or at the microscopic level. It features an inner coaxial tube which delivers a harvesting fluid into the very tip of the collecting needle, permitting metabolic activity in the sample to be quenched immediately. The device is easily constructed from common laboratory material.     

Determination of protein-ligand binding constants at equilibrium in biological samples.

Protein-ligand complexes can be separated functionally into two classes. "Specific" binding is characterized, in relative terms, by a high affinity for the ligand and a low binding capacity. "Non-specific" binding is characterized by a low affinity and a very large capacity. The calculation of equilibrium binding constants for any specific protein-ligand interaction requires the exact determination of the unbound ligand concentration and the specifically bound ligand concentration. These determinations usually require corrections for the contribution of non-specific binding. The use of two correction terms, kn and f, is proposed: kn is the product of the affinity constant k times the number of binding sites n of the non-specific components, while f is the fraction of the non-specific binding included in the experimental estimates of bound ligand. Several theoretical solutions using these terms are proposed for the calculation of specific binding constants. The practical choice of the correction factor may be different when the simultaneous measurement of the affinity constant and maximum number of binding sites, or when only the latter, is desired. In the case of complex binding systesm containing more than one specific component, the individual constants can be determined by non-graphical methods, using computer-aided iterative statistical calculations. A complete solution is given for a system containing two specific plus non-specific interactions and actual experiments are reported for steroid hormone-receptro complexes.     

不同倍性鱼的血细胞和精子DNA含量比较

我们以前的研究表明, 以红鲫 (2n=100) 为母本及湘江野鲤 (2n=100) 为父本的杂交后代的F1-F2 为二倍体 (2n= 100)。在二倍体 F2 个体中, 存在能分别产生二倍体卵子和二倍体精子的雌、雄个体, 二倍体卵子和二倍体精子结合, 形成了两性可育的四倍体鱼 (F3)。目前四倍体鲫鲤已连续繁殖了 12 代 (F3-F14), 形成了一个遗传性状稳定的四倍体鱼群体 (4n= 200) (Liu et al.,2001; 孙远东等, 2003)。雌性四倍体鲫鲤产生的二倍体卵子经紫外线照射的散鳞镜鲤精子激活后,无须染色体加倍处理, 可发育为全雌性二倍体雌核发育后代 (G1) (2n=10…     

Discovering functions and revealing mechanisms at molecular level from biological networks

With the increasingly accumulated data from high-throughput technologies, study on biomolecular networks has become one of key focuses in systems biology and bioinformatics. In particular, various types of molecular networks (e.g., protein-protein interaction (PPI) network; gene regulatory network (GRN); metabolic network (MN); gene coexpression network (GCEN)) have been extensively investigated, and those studies demonstrate great potentials to discover basic functions and to reveal essential mechanisms for various biological phenomena, by understanding biological systems not at individual component level but at a system-wide level. Recent studies on networks have created very prolific researches on many aspects of living organisms. In this paper, we aim to review the recent developments on topics related to molecular networks in a comprehensive manner, with the special emphasis on the computational aspect. The contents of the survey cover global topological properties and local structural characteristics, network motifs, network comparison and query, detection of functional modules and network motifs, function prediction from network analysis, inferring molecular networks from biological data as well as representative databases and software tools.     

Comparison of the biological effects of F at different intracellular levels

We herein examined the biological effects of cells treated with ¹⁸F labeled drugs for positron emission tomography (PET). The relationship between the intracellular distribution of ¹⁸F and levels of damaged DNA has yet to be clarified in detail. We used culture cells (Chinese Hamster Ovary cells) treated with two types of ¹⁸F labeled drugs, fluorodeoxyglucose (FDG) and fluorine ion (HF). FDG efficiently accumulated in cells, whereas HF did not. To examine the induction of DNA double strand breaks (DSB), we measured the number of foci for 53BP1 that formed at the site of DNA DSB. The results revealed that although radioactivity levels were the same, the induction of 53BP1 foci was stronger in cells treated with ¹⁸F-FDG than in those treated with ¹⁸F-HF. The clonogenic survival of cells was significantly lower with ¹⁸F-FDG than with ¹⁸F-HF. We concluded that the efficient accumulation of ¹⁸F in cells led to stronger biological effects due to more severe cellular lethality via the induction of DNA DSB.     

Neutron activation analysis of biological samples at the Radiochemistry Division of IPEN-CNEN/SP

Biological Trace Element Research - Neutron activation analysis is a very useful method for determination of a great number of elements in biological samples. At the Radiochemistry Division of the...